1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head><meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<title>OBElementTable Class Reference</title>
<link href="/site.css" rel="stylesheet" type="text/css">
<link href="doxygen.css" rel="stylesheet" type="text/css">
<link href="tabs.css" rel="stylesheet" type="text/css">
<script type="text/javascript" src="search/search.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<!--#include file="header.html" -->
<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.shtml"><span>Main Page</span></a></li>
<li><a href="pages.shtml"><span>Related Pages</span></a></li>
<li><a href="modules.shtml"><span>Modules</span></a></li>
<li><a href="namespaces.shtml"><span>Namespaces</span></a></li>
<li class="current"><a href="annotated.shtml"><span>Classes</span></a></li>
<li><a href="files.shtml"><span>Files</span></a></li>
<li><a href="examples.shtml"><span>Examples</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="annotated.shtml"><span>Class List</span></a></li>
<li><a href="classes.shtml"><span>Class Index</span></a></li>
<li><a href="hierarchy.shtml"><span>Class Hierarchy</span></a></li>
<li><a href="functions.shtml"><span>Class Members</span></a></li>
</ul>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a> </li>
<li class="navelem"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml">OBElementTable</a> </li>
</ul>
</div>
</div>
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> </div>
<div class="headertitle">
<div class="title">OBElementTable Class Reference</div> </div>
</div>
<div class="contents">
<!-- doxytag: class="OpenBabel::OBElementTable" --><!-- doxytag: inherits="OpenBabel::OBGlobalDataBase" -->
<p><code>#include <<a class="el" href="data_8h_source.shtml">openbabel/data.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for OBElementTable:</div>
<div class="dyncontent">
<div class="center"><img src="classOpenBabel_1_1OBElementTable__inherit__graph.png" border="0" usemap="#OBElementTable_inherit__map" alt="Inheritance graph"/></div>
<map name="OBElementTable_inherit__map" id="OBElementTable_inherit__map">
<area shape="rect" id="node2" href="classOpenBabel_1_1OBGlobalDataBase.shtml" title="Base data table class, handles reading data files." alt="" coords="5,5,155,35"/></map>
<center><span class="legend">[<a href="graph_legend.shtml">legend</a>]</span></center></div>
<p><a href="classOpenBabel_1_1OBElementTable-members.shtml">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a87bb51173627999f7648500e25896dad">OBElementTable</a> (void)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a47b05df47eb3884d0c951f65727d8022">~OBElementTable</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#ae59fef8af62e52629bf2576e34a26801">ParseLine</a> (const char *)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">unsigned int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a656877a45442ec49f7410896abd65ac8">GetNumberOfElements</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#aab7c531e5ffc5174e57a85e853931534">GetSize</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a8228e8800bb8fae4658c751d6e999918">GetAtomicNum</a> (const char *)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a4f3c95b233fb0842946292b984acf1a3">GetAtomicNum</a> (const char *, int &iso)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a171c098398572c552e88be4e703127bb">GetAtomicNum</a> (std::string name, int &iso)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405">GetSymbol</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a5534d1a7688c45521d2fee711d5a304b">GetVdwRad</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a77199f1c422c616646ba373e1d79e485">GetCovalentRad</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a77ac743193728f2c07da8d84cc0f60e7">GetMass</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#ae62d275baa205c4838fb498429d906e1">CorrectedBondRad</a> (int, int=3)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#af05f1d98b5f08cad58d6e1b41976e7b7">CorrectedVdwRad</a> (int, int=3)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a130b6cb6f0bee924e3f183d607200f2f">GetMaxBonds</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#ad7d453967ce8286a47aae29825f22cc5">GetElectroNeg</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#af8ffe9fb539c2e7222c0f9df2a05d612">GetAllredRochowElectroNeg</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a891e482e56f4a74680df62002b4eef23">GetIonization</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a440d72ea4b65b4d6fed724e47db623fc">GetElectronAffinity</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a6bec3afa386bc2df86bc1c59a2b0396e">GetRGB</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml#aea00d52050ec324fef7c792567341c09">GetName</a> (int)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a1e3b6d38df0786ccf7f938d60e386aae">Init</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a49002f92ad6a1c71d7f9148271770b7a">SetReadDirectory</a> (char *dir)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a2bd0630d27e20f38de4c753ca68e2282">SetEnvironmentVariable</a> (char *var)</td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a40756214f69d1c40ad70b64ae9fdc08d">_init</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a45a08560f2b4885250c586c550f2d7af">_dataptr</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a895aefe990ffe9af66bb5cd4e37d3579">_filename</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a2c2f62a9907553e5feb1ecef65c6c386">_dir</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a5d93159b6eee0cb302451621106f61c7">_subdir</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a87d06c3aed77fb9e118b337bed557928">_envvar</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Periodic Table of the Elements. </p>
<p>Translating element data is a common task given that many file formats give either element symbol or atomic number information, but not both. The <a class="el" href="classOpenBabel_1_1OBElementTable.shtml" title="Periodic Table of the Elements.">OBElementTable</a> class facilitates conversion between textual and numeric element information. An instance of the <a class="el" href="classOpenBabel_1_1OBElementTable.shtml" title="Periodic Table of the Elements.">OBElementTable</a> class (etab) is declared as external in <a class="el" href="data_8cpp.shtml" title="Global data and resource file parsers.">data.cpp</a>. Source files that include the header file <a class="el" href="mol_8h.shtml" title="Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. (the main header for Open Babel)...">mol.h</a> automatically have an extern definition to etab. The following code sample demonstrates the use of the <a class="el" href="classOpenBabel_1_1OBElementTable.shtml" title="Periodic Table of the Elements.">OBElementTable</a> class: </p>
<div class="fragment"><pre class="fragment"> cout << <span class="stringliteral">"The symbol for element 6 is "</span> << <a class="code" href="namespaceOpenBabel.shtml#a1e53ca6bf87ac2f6447c9ef2332c9418" title="Global OBElementTable for element properties.">etab</a>.GetSymbol(6) << endl;
cout << <span class="stringliteral">"The atomic number for Sulfur is "</span> << <a class="code" href="namespaceOpenBabel.shtml#a1e53ca6bf87ac2f6447c9ef2332c9418" title="Global OBElementTable for element properties.">etab</a>.GetAtomicNum(16) << endl;
cout << <span class="stringliteral">"The van der Waal radius for Nitrogen is "</span> << <a class="code" href="namespaceOpenBabel.shtml#a1e53ca6bf87ac2f6447c9ef2332c9418" title="Global OBElementTable for element properties.">etab</a>.GetVdwRad(7);
</pre></div><p>Stored information in the <a class="el" href="classOpenBabel_1_1OBElementTable.shtml" title="Periodic Table of the Elements.">OBElementTable</a> includes elemental:</p>
<ul>
<li>symbols</li>
<li>covalent radii</li>
<li>van der Waal radii</li>
<li>expected maximum bonding valence</li>
<li>molar mass (by IUPAC recommended atomic masses)</li>
<li>electronegativity (Pauling and Allred-Rochow)</li>
<li>ionization potential</li>
<li>electron affinity</li>
<li>RGB colors for visualization programs</li>
<li>names (by IUPAC recommendation) </li>
</ul>
</div><hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a87bb51173627999f7648500e25896dad"></a><!-- doxytag: member="OpenBabel::OBElementTable::OBElementTable" ref="a87bb51173627999f7648500e25896dad" args="(void)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classOpenBabel_1_1OBElementTable.shtml">OBElementTable</a> </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
</div>
</div>
<a class="anchor" id="a47b05df47eb3884d0c951f65727d8022"></a><!-- doxytag: member="OpenBabel::OBElementTable::~OBElementTable" ref="a47b05df47eb3884d0c951f65727d8022" args="()" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">~<a class="el" href="classOpenBabel_1_1OBElementTable.shtml">OBElementTable</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="ae59fef8af62e52629bf2576e34a26801"></a><!-- doxytag: member="OpenBabel::OBElementTable::ParseLine" ref="ae59fef8af62e52629bf2576e34a26801" args="(const char *)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void ParseLine </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"></td><td>)</td>
<td><code> [virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Specified by particular table classes (parses an individual data line) </p>
<p>Reimplemented from <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a9a84dbfb089769dec48cd6f6eca1057b">OBGlobalDataBase</a>.</p>
</div>
</div>
<a class="anchor" id="a656877a45442ec49f7410896abd65ac8"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetNumberOfElements" ref="a656877a45442ec49f7410896abd65ac8" args="()" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">unsigned int GetNumberOfElements </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the number of elements in the periodic table </dd></dl>
</div>
</div>
<a class="anchor" id="aab7c531e5ffc5174e57a85e853931534"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetSize" ref="aab7c531e5ffc5174e57a85e853931534" args="()" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">size_t GetSize </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td><code> [inline, virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the number of elements in the periodic table </dd></dl>
<p>Reimplemented from <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a5ebfe2dd02a8ba2b7e84f1f6d55c74cd">OBGlobalDataBase</a>.</p>
</div>
</div>
<a class="anchor" id="a8228e8800bb8fae4658c751d6e999918"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetAtomicNum" ref="a8228e8800bb8fae4658c751d6e999918" args="(const char *)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int GetAtomicNum </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>sym</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="deprecated"><dt><b><a class="el" href="deprecated.shtml#_deprecated000035">Deprecated:</a></b></dt><dd>Does not properly handle 'D' or 'T' hydrogen isotopes </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1AliasData.shtml#ae9370e865e83b4dfefbb8b6cb2c15535">AliasData::Expand()</a>.</p>
</div>
</div>
<a class="anchor" id="a4f3c95b233fb0842946292b984acf1a3"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetAtomicNum" ref="a4f3c95b233fb0842946292b984acf1a3" args="(const char *, int &iso)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int GetAtomicNum </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>identifier</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int & </td>
<td class="paramname"><em>iso</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the atomic number matching the element symbol or IUPAC name passed or 0 if not defined. For 'D' or 'T' hydrogen isotopes, will return a value in the second argument </dd></dl>
</div>
</div>
<a class="anchor" id="a171c098398572c552e88be4e703127bb"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetAtomicNum" ref="a171c098398572c552e88be4e703127bb" args="(std::string name, int &iso)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int GetAtomicNum </td>
<td>(</td>
<td class="paramtype">std::string </td>
<td class="paramname"><em>name</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int & </td>
<td class="paramname"><em>iso</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Overloads <a class="el" href="classOpenBabel_1_1OBElementTable.shtml#a4f3c95b233fb0842946292b984acf1a3">GetAtomicNum(const char *, int &iso)</a> </p>
</div>
</div>
<a class="anchor" id="a18907ad1590deb926b43c4f08cac9405"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetSymbol" ref="a18907ad1590deb926b43c4f08cac9405" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">const char * GetSymbol </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the element symbol matching the atomic number passed </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBDepict.shtml#a9ef29e99771a1932b2c28b34533a3e96">OBDepict::DrawMolecule()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a997bc4b84a93d285f63efa60cbb8ee8d">OBMol::GetSpacedFormula()</a>.</p>
</div>
</div>
<a class="anchor" id="a5534d1a7688c45521d2fee711d5a304b"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetVdwRad" ref="a5534d1a7688c45521d2fee711d5a304b" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetVdwRad </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the van der Waals radius for this atomic number </dd></dl>
</div>
</div>
<a class="anchor" id="a77199f1c422c616646ba373e1d79e485"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetCovalentRad" ref="a77199f1c422c616646ba373e1d79e485" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetCovalentRad </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the covalent radius for this atomic number </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBMol.shtml#a31d05972f7454e791641c4a7d0071d12">OBMol::ConnectTheDots()</a>.</p>
</div>
</div>
<a class="anchor" id="a77ac743193728f2c07da8d84cc0f60e7"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetMass" ref="a77ac743193728f2c07da8d84cc0f60e7" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetMass </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the average atomic mass for this element. For exact isotope masses, use <a class="el" href="classOpenBabel_1_1OBIsotopeTable.shtml" title="Table of atomic isotope masses.">OpenBabel::OBIsotopeTable</a> </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a635bb1edc5190cbe33eda4a34843be9b">OBAtom::GetAtomicMass()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#a77cd52b60b431c19aa7debcd0d92e07d">OBMol::GetMolWt()</a>.</p>
</div>
</div>
<a class="anchor" id="ae62d275baa205c4838fb498429d906e1"></a><!-- doxytag: member="OpenBabel::OBElementTable::CorrectedBondRad" ref="ae62d275baa205c4838fb498429d906e1" args="(int, int=3)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double CorrectedBondRad </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>hyb</em> = <code>3</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>a "corrected" bonding radius based on the hybridization. Scales the covalent radius by 0.95 for sp2 and 0.90 for sp hybrids </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBMol.shtml#ad3bab31bf64ff6cb18f6ee259b3b8c11">OBMol::AddHydrogens()</a>, <a class="el" href="namespaceOpenBabel.shtml#a69c4665c3756720ac6f0d62b2488fdd6">OpenBabel::GetCorrectedBondVector()</a>, <a class="el" href="classOpenBabel_1_1OBBond.shtml#a5a63a8b7f30958105ce72602da6715e9">OBBond::GetEquibLength()</a>, <a class="el" href="classOpenBabel_1_1OBAtom.shtml#a51618686d8ad1b5f66ff2fc2c607493e">OBAtom::HtoMethyl()</a>, <a class="el" href="classOpenBabel_1_1OBMol.shtml#ac749cfb04173f6f35ef64b1ac1d87178">OBMol::PerceiveBondOrders()</a>, and <a class="el" href="classOpenBabel_1_1OBAtom.shtml#af7a144a4ef755d5cc31e0d2e47a2e84a">OBAtom::SetHybAndGeom()</a>.</p>
</div>
</div>
<a class="anchor" id="af05f1d98b5f08cad58d6e1b41976e7b7"></a><!-- doxytag: member="OpenBabel::OBElementTable::CorrectedVdwRad" ref="af05f1d98b5f08cad58d6e1b41976e7b7" args="(int, int=3)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double CorrectedVdwRad </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>hyb</em> = <code>3</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>a "corrected" vdW radius based on the hybridization. Scales the van der Waals radius by 0.95 for sp2 and 0.90 for sp hybrids </dd></dl>
</div>
</div>
<a class="anchor" id="a130b6cb6f0bee924e3f183d607200f2f"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetMaxBonds" ref="a130b6cb6f0bee924e3f183d607200f2f" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int GetMaxBonds </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the maximum expected number of bonds to this element </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBMol.shtml#a31d05972f7454e791641c4a7d0071d12">OBMol::ConnectTheDots()</a>, and <a class="el" href="classOpenBabel_1_1OBMol.shtml#ac749cfb04173f6f35ef64b1ac1d87178">OBMol::PerceiveBondOrders()</a>.</p>
</div>
</div>
<a class="anchor" id="ad7d453967ce8286a47aae29825f22cc5"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetElectroNeg" ref="ad7d453967ce8286a47aae29825f22cc5" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetElectroNeg </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the Pauling electronegativity for this element </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBMol.shtml#ac749cfb04173f6f35ef64b1ac1d87178">OBMol::PerceiveBondOrders()</a>.</p>
</div>
</div>
<a class="anchor" id="af8ffe9fb539c2e7222c0f9df2a05d612"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetAllredRochowElectroNeg" ref="af8ffe9fb539c2e7222c0f9df2a05d612" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetAllredRochowElectroNeg </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the Allred-Rochow electronegativity for this element </dd></dl>
</div>
</div>
<a class="anchor" id="a891e482e56f4a74680df62002b4eef23"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetIonization" ref="a891e482e56f4a74680df62002b4eef23" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetIonization </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the ionization potential (in eV) for this element </dd></dl>
</div>
</div>
<a class="anchor" id="a440d72ea4b65b4d6fed724e47db623fc"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetElectronAffinity" ref="a440d72ea4b65b4d6fed724e47db623fc" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">double GetElectronAffinity </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the electron affinity (in eV) for this element </dd></dl>
</div>
</div>
<a class="anchor" id="a6bec3afa386bc2df86bc1c59a2b0396e"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetRGB" ref="a6bec3afa386bc2df86bc1c59a2b0396e" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">vector< double > GetRGB </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>a vector with red, green, blue color values for this element </dd></dl>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBDepict.shtml#a9ef29e99771a1932b2c28b34533a3e96">OBDepict::DrawMolecule()</a>.</p>
</div>
</div>
<a class="anchor" id="aea00d52050ec324fef7c792567341c09"></a><!-- doxytag: member="OpenBabel::OBElementTable::GetName" ref="aea00d52050ec324fef7c792567341c09" args="(int)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">string GetName </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>atomicnum</em></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>the name of this element </dd></dl>
</div>
</div>
<a class="anchor" id="a1e3b6d38df0786ccf7f938d60e386aae"></a><!-- doxytag: member="OpenBabel::OBElementTable::Init" ref="a1e3b6d38df0786ccf7f938d60e386aae" args="()" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void Init </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td><code> [inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Read in the data file, falling back as needed. </p>
</div>
</div>
<a class="anchor" id="a49002f92ad6a1c71d7f9148271770b7a"></a><!-- doxytag: member="OpenBabel::OBElementTable::SetReadDirectory" ref="a49002f92ad6a1c71d7f9148271770b7a" args="(char *dir)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void SetReadDirectory </td>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>dir</em></td><td>)</td>
<td><code> [inline, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the directory before calling <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a1e3b6d38df0786ccf7f938d60e386aae" title="Read in the data file, falling back as needed.">Init()</a> </p>
</div>
</div>
<a class="anchor" id="a2bd0630d27e20f38de4c753ca68e2282"></a><!-- doxytag: member="OpenBabel::OBElementTable::SetEnvironmentVariable" ref="a2bd0630d27e20f38de4c753ca68e2282" args="(char *var)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void SetEnvironmentVariable </td>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>var</em></td><td>)</td>
<td><code> [inline, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the environment variable to use before calling <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a1e3b6d38df0786ccf7f938d60e386aae" title="Read in the data file, falling back as needed.">Init()</a> </p>
</div>
</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a40756214f69d1c40ad70b64ae9fdc08d"></a><!-- doxytag: member="OpenBabel::OBElementTable::_init" ref="a40756214f69d1c40ad70b64ae9fdc08d" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a40756214f69d1c40ad70b64ae9fdc08d">_init</a><code> [protected, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Whether the data been read already. </p>
</div>
</div>
<a class="anchor" id="a45a08560f2b4885250c586c550f2d7af"></a><!-- doxytag: member="OpenBabel::OBElementTable::_dataptr" ref="a45a08560f2b4885250c586c550f2d7af" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">const char* <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a45a08560f2b4885250c586c550f2d7af">_dataptr</a><code> [protected, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Default data table if file is unreadable. </p>
</div>
</div>
<a class="anchor" id="a895aefe990ffe9af66bb5cd4e37d3579"></a><!-- doxytag: member="OpenBabel::OBElementTable::_filename" ref="a895aefe990ffe9af66bb5cd4e37d3579" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">std::string <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a895aefe990ffe9af66bb5cd4e37d3579">_filename</a><code> [protected, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>File to search for. </p>
</div>
</div>
<a class="anchor" id="a2c2f62a9907553e5feb1ecef65c6c386"></a><!-- doxytag: member="OpenBabel::OBElementTable::_dir" ref="a2c2f62a9907553e5feb1ecef65c6c386" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">std::string <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a2c2f62a9907553e5feb1ecef65c6c386">_dir</a><code> [protected, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Data directory for file if _envvar fails. </p>
</div>
</div>
<a class="anchor" id="a5d93159b6eee0cb302451621106f61c7"></a><!-- doxytag: member="OpenBabel::OBElementTable::_subdir" ref="a5d93159b6eee0cb302451621106f61c7" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">std::string <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a5d93159b6eee0cb302451621106f61c7">_subdir</a><code> [protected, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Subdirectory (if using environment variable) </p>
</div>
</div>
<a class="anchor" id="a87d06c3aed77fb9e118b337bed557928"></a><!-- doxytag: member="OpenBabel::OBElementTable::_envvar" ref="a87d06c3aed77fb9e118b337bed557928" args="" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">std::string <a class="el" href="classOpenBabel_1_1OBGlobalDataBase.shtml#a87d06c3aed77fb9e118b337bed557928">_envvar</a><code> [protected, inherited]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Environment variable to check first. </p>
</div>
</div>
<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="data_8h_source.shtml">data.h</a></li>
<li><a class="el" href="data_8cpp.shtml">data.cpp</a></li>
</ul>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark"> </span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark"> </span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark"> </span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark"> </span>Friends</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(10)"><span class="SelectionMark"> </span>Defines</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
</div><!-- end content -->
<!--#include file="footer.html" -->
<div id="footer">
<hr size="1">
<img src="http://openbabel.org/babel256.png" width="136" height="127" alt="" style="float: left;" />
<p>This file is part of the documentation for <a href="http://openbabel.org/wiki/">Open Babel</a>, version 2.3.</p>
<div class="bottom">
Documentation copyright © 1998-2007, the <a href="http://openbabel.org/wiki/THANKS">Open Babel Developers</a>.<br>
Open Babel is hosted by: <a href="http://sourceforge.net">
<img src="http://sourceforge.net/sflogo.php?group_id=40728"
width="88" height="31" border="0" alt="SourceForge Logo"></a><br>
Generated on Thu Oct 13 2011 16:08:09 by <a href="http://www.doxygen.org/"><img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.7.5.1.
</div>
</body>
</html>
|
